| d44ef78 | Thomas B. Mooney | 23 March 2015, 19:26:18 UTC | Merge pull request #530 from tmooney/print_useful_message_on_fl_update Print the display name for blessed objects. | 23 March 2015, 19:26:18 UTC |
| fb73f4d | David Morton | 23 March 2015, 16:05:03 UTC | Merge pull request #575 from mkiwala/initial-ptero-integration Initial ptero integration | 23 March 2015, 16:05:03 UTC |
| c05d89c | Michael J. Kiwala | 23 March 2015, 15:14:56 UTC | Do not compare "user" lines from the resulting json | 23 March 2015, 15:14:56 UTC |
| a98a522 | Michael J. Kiwala | 23 March 2015, 14:32:52 UTC | Make call to WfBuilder execute() compatible with new function signature | 23 March 2015, 14:32:52 UTC |
| 59d8f85 | Michael J. Kiwala | 23 March 2015, 14:12:13 UTC | Remove useless check for empty GENOME_ env var GENOME_WORKFLOW_BUILDER_BACKEND already has a default specified in Env::GENOME_WORKFLOW_BUILDER_BACKEND. | 23 March 2015, 14:12:13 UTC |
| 04b0296 | Michael J. Kiwala | 23 March 2015, 14:11:21 UTC | Replace access of $ENV{USER} with call to Genome::Sys->username | 23 March 2015, 14:11:21 UTC |
| 1ff49a6 | APipe Tester | 22 March 2015, 12:18:32 UTC | Updated `gmt` tab completion. | 22 March 2015, 12:18:32 UTC |
| 2cf8e41 | APipe Tester | 22 March 2015, 12:17:32 UTC | Updated `genome` tab completion. | 22 March 2015, 12:17:32 UTC |
| 3a1dae1 | David Morton | 19 March 2015, 02:03:58 UTC | error_message natively supports sprintf formatting | 20 March 2015, 18:38:21 UTC |
| 73ce1b6 | Michael J. Kiwala | 17 March 2015, 19:51:56 UTC | Change Carp::confess to die Conflicts: lib/perl/Genome/WorkflowBuilder/DAG.pm | 20 March 2015, 18:38:08 UTC |
| 370ae33 | Michael J. Kiwala | 17 March 2015, 19:45:26 UTC | Make requires reference the specific Ptero modules needed | 20 March 2015, 18:38:03 UTC |
| 4dde6e0 | David Morton | 19 March 2015, 01:59:45 UTC | Allow WorkflowBuilder to submit to PTero | 20 March 2015, 18:37:42 UTC |
| cbdac0a | David Morton | 19 March 2015, 01:14:24 UTC | Allow for multiple WorkflowBuilder backends The interface for the 'execute' method changes here as well. The old interface was to accept any number of named arguments, but this makes it so that the interface cannot be extended in the future. If one were to ever want to add an optional argument to execute, it would collide with the workflow inputs. | 20 March 2015, 18:22:38 UTC |
| 4356fd5 | Indraniel | 20 March 2015, 15:55:48 UTC | Merge pull request #568 from indraniel/ercc-map-unaligned-experiment-pt2 ERCC-based Quality Control Screening for RNASeq: Part 2 | 20 March 2015, 15:55:48 UTC |
| b968c86 | Indraniel Das | 20 March 2015, 15:38:48 UTC | + make "% Mapped" be a real percentage - the number should be from [0,1], but rather [0, 100]. | 20 March 2015, 15:38:48 UTC |
| 0527802 | APipe Tester | 20 March 2015, 12:20:08 UTC | Updated `gmt` tab completion. | 20 March 2015, 12:20:08 UTC |
| 1850df5 | APipe Tester | 20 March 2015, 12:19:05 UTC | Updated `genome` tab completion. | 20 March 2015, 12:19:05 UTC |
| b699197 | APipe Tester | 20 March 2015, 12:16:36 UTC | Updated class browser cache. | 20 March 2015, 12:16:36 UTC |
| 8fc9d7a | Thomas B. Mooney | 19 March 2015, 22:09:43 UTC | Merge pull request #572 from tmooney/less_stratospheric_memory_limits Match -M to actual resource requests. | 19 March 2015, 22:09:43 UTC |
| da48ab3 | Indraniel Das | 19 March 2015, 20:43:02 UTC | + fix p-value Mix label typo | 19 March 2015, 20:43:02 UTC |
| 89048b0 | Indraniel Das | 19 March 2015, 20:08:38 UTC | + use the genome allocated version of the ERCC_Controls_Analysis.txt - this currently the advised way to handle this file | 19 March 2015, 20:08:38 UTC |
| 68872bb | Indraniel Das | 19 March 2015, 19:48:52 UTC | + apply @jasonwalker80 's 4th recommendation (PR 568) - Jason mention to show the ERCC re-alignment statistics in the outputs. See comment in BIO-1345. | 19 March 2015, 19:53:15 UTC |
| 34b3fde | Indraniel Das | 19 March 2015, 19:45:51 UTC | + let generate_idxstats return the file not data hash - let the 'generate_tsvfile' method get the data hash elements. This is for a refactoring to introduce alignment statistics in the outputs. See the next commit about it. | 19 March 2015, 19:53:14 UTC |
| 0c1f9e2 | Indraniel Das | 18 March 2015, 23:59:59 UTC | + apply @jasonwalker80 's 3rd recommendation (PR 568) - refine the outputs of the R Script: include the results of the statistical tests applied - Highlight what the automated system thinks the mixture is via the "DECISION: " line. - refine what message gets outputted when the automated system has trouble making a decision. - Adjust the output formatting into sections ("Tables", "Tests", & "Plots). - See comment in BIO-1345. | 19 March 2015, 19:52:57 UTC |
| 067e9c5 | Indraniel Das | 18 March 2015, 23:19:16 UTC | + apply @jasonwalker80 's 2nd recommendation (PR 568) - change the "Probability" column name to "ExpectedMixRatios" This is a better term for the end users. See comment in BIO-1345. | 19 March 2015, 19:52:39 UTC |
| ea07844 | Indraniel Das | 18 March 2015, 23:15:27 UTC | + apply @jasonwalker80 's 1st recommendation (PR 568) - use a reference sequence that's recorded in the genome system. This is the same ERCC reference sequence as before, but has been appended to an existing imported reference sequence. | 19 March 2015, 19:52:09 UTC |
| 062c46c | Avinash Ramu | 19 March 2015, 15:57:08 UTC | Merge pull request #531 from gatoravi/somaticfilter_workflow somatic-filter workflow | 19 March 2015, 15:57:08 UTC |
| 841f4ce | Thomas B. Mooney | 19 March 2015, 15:16:48 UTC | Merge pull request #569 from tmooney/harmonize_dv2_dispatcher_resources Set tmp and mem requests for DV2 dispatchers | 19 March 2015, 15:16:48 UTC |
| 84947b1 | Thomas B. Mooney | 19 March 2015, 15:09:19 UTC | Merge pull request #570 from tmooney/lower_false_indel_memory_requests Lower false indel memory requests | 19 March 2015, 15:09:19 UTC |
| 821951c | Indraniel Das | 18 March 2015, 23:04:58 UTC | + reapply @acoffman 's earlier suggestion - somehow I lost @acoffman's original file existence modifications from an earlier commit. Perhaps it got "Lost in Refactoring". | 18 March 2015, 23:04:58 UTC |
| a1c52ff | Indraniel Das | 18 March 2015, 18:28:25 UTC | + re-enable the SKIP block on the test. - I momentarily removed the SKIP block to test out the "model" to "build" input parameter change. | 18 March 2015, 21:12:16 UTC |
| 5464fae | Indraniel Das | 18 March 2015, 18:22:35 UTC | + apply @tmooney 's 3rd recommendation (PR 568) - use the "die $self->error_message" idiom. According to @tmooney, the genome system makes better error output decisions when using this approach. | 18 March 2015, 21:12:15 UTC |
| c687964 | Nathaniel Nutter | 18 March 2015, 21:07:29 UTC | Merge pull request #571 from nnutter/AR-953 re-enable Abyss.t | 18 March 2015, 21:07:29 UTC |
| 402580e | Thomas Mooney | 18 March 2015, 20:55:14 UTC | Match memlimit to resource requests. | 18 March 2015, 20:55:14 UTC |
| 4fc825f | Thomas B. Mooney | 18 March 2015, 20:13:47 UTC | Merge pull request #566 from tmooney/composite_workflow_v3 Split Apart G:ID:Composite::Workflow | 18 March 2015, 20:13:47 UTC |
| eb85725 | Nathaniel Nutter | 18 March 2015, 20:02:51 UTC | re-enable Abyss.t | 18 March 2015, 20:03:58 UTC |
| f6b42ec | Indraniel Das | 18 March 2015, 18:18:36 UTC | + apply @tmooney 's 2nd recommendation (PR 568) - have the user supply a 'build' as an input rather than a 'model' This is more granular. Additionally as @tmooney described to me, if the user supplies a model id instead, there is internal logic in the genome system to bring up an interactive prompt to choose which build from the model to use. This way the user can supply either a model or build id as an input parameter. - While making this change we also refactored the "setup_pdf_file" and "setup_raw_stats_file" methods. A new "setup_output_file" method was added and common logic between "setup_pdf_file" and "setup_raw_stats_file" was placed into ther. | 18 March 2015, 18:31:33 UTC |
| 220af59 | Indraniel Das | 18 March 2015, 18:12:39 UTC | + apply @tmooney 's 1st recommendation (PR 568) - remove the needless example_values, when a default_value is present. | 18 March 2015, 18:30:12 UTC |
| d42efca | Eddie Belter | 18 March 2015, 17:55:26 UTC | Merge pull request #567 from ebelter/instdata-import InstData Import: make anp required in workflow step | 18 March 2015, 17:55:26 UTC |
| acd55e4 | Indraniel | 18 March 2015, 16:54:55 UTC | Merge pull request #1 from acoffman/ercc-map-unaligned-experiment-pt2 Simplify bam path acquistion. | 18 March 2015, 16:54:55 UTC |
| 8d7beec | Adam Coffman | 18 March 2015, 15:51:48 UTC | only check for file existence in a single location | 18 March 2015, 15:51:48 UTC |
| 8af6ed2 | Adam Coffman | 18 March 2015, 15:39:20 UTC | only instantiate the bam File object in a single place | 18 March 2015, 15:39:20 UTC |
| 3e9a6ae | APipe Tester | 18 March 2015, 15:39:00 UTC | updated ur submodule to c80b913 | 18 March 2015, 15:39:00 UTC |
| f4f33b6 | Adam Coffman | 18 March 2015, 15:31:19 UTC | whitespace | 18 March 2015, 15:31:19 UTC |
| a616960 | Thomas Mooney | 18 March 2015, 15:05:56 UTC | Lower default memory request. Running "false-indel" after samtools would require a lot of RAM (hence the 32GB request), but we no longer run this filter on samtools indels. | 18 March 2015, 15:05:56 UTC |
| 8d68686 | Thomas Mooney | 18 March 2015, 15:05:37 UTC | Whitespace. | 18 March 2015, 15:05:37 UTC |
| fb4da3a | Thomas Mooney | 18 March 2015, 13:35:44 UTC | Harmonize temp requests. (The LQ Union step following the WF uses tmp to create the union file.) | 18 March 2015, 13:41:19 UTC |
| 9c2e4c8 | Thomas Mooney | 18 March 2015, 13:33:37 UTC | Set lower memory limit for DV2 dispatchers. A survey of jobs over the past two weeks showed none used > 200 MB. | 18 March 2015, 13:41:18 UTC |
| 80c3852 | APipe Tester | 18 March 2015, 12:17:34 UTC | Updated `gmt` tab completion. | 18 March 2015, 12:17:34 UTC |
| 54430da | APipe Tester | 18 March 2015, 12:16:46 UTC | Updated `genome` tab completion. | 18 March 2015, 12:16:46 UTC |
| 039c831 | APipe Tester | 18 March 2015, 12:15:01 UTC | Updated class browser cache. | 18 March 2015, 12:15:01 UTC |
| edc94b8 | Thomas Mooney | 17 March 2015, 21:21:46 UTC | Include all errors; not just the first. | 17 March 2015, 21:21:46 UTC |
| 9ef6c8e | Indraniel Das | 17 March 2015, 21:05:17 UTC | + check if the input bam file exists before proceeding | 17 March 2015, 21:09:37 UTC |
| 26b0a56 | Indraniel Das | 17 March 2015, 21:02:19 UTC | + only --model or --bam-file can be used, not both - error out if the user supplies both options | 17 March 2015, 21:09:37 UTC |
| 9437cb2 | Indraniel Das | 17 March 2015, 20:58:45 UTC | + update model comments in test | 17 March 2015, 21:09:36 UTC |
| b7e794e | Indraniel Das | 17 March 2015, 20:56:56 UTC | + adjust the number of tests done in SKIP block | 17 March 2015, 21:09:35 UTC |
| 200a256 | Indraniel Das | 17 March 2015, 20:54:40 UTC | + pass in the model directly in the test | 17 March 2015, 21:09:35 UTC |
| cd98c4c | Indraniel Das | 17 March 2015, 20:52:47 UTC | + if the raw_stat_file already exists remove it - just simply copy over the original raw_stat_file if it already exists. | 17 March 2015, 21:09:34 UTC |
| 959dbe9 | Indraniel Das | 17 March 2015, 20:51:07 UTC | + remove the ercc_spike_in_mix input parameter - no longer makes sense to specify it. the R analysis script uses both mixes to identify which one was used. | 17 March 2015, 21:09:34 UTC |
| fbf26aa | Indraniel Das | 17 March 2015, 20:48:13 UTC | + make the ercc_fasta_file input optional - place a default value of @jasonwalker80 originally mentioned path | 17 March 2015, 21:09:31 UTC |
| 5aba541 | Indraniel Das | 17 March 2015, 20:45:30 UTC | + customize the inputs and outputs of the tool - be able to accept either a model or a bam_file directly as input - based on the model or bam_file input construct appropriate names for the desired outputs: the pdf_file and the raw_stats_file | 17 March 2015, 21:09:31 UTC |
| c0788c8 | Indraniel Das | 17 March 2015, 20:40:29 UTC | + rename R function - 'make.LinearityPlot' -> 'linearity.plot' make it similar to the other plot function (mix.plot) | 17 March 2015, 21:09:29 UTC |
| 68d0120 | Indraniel Das | 17 March 2015, 16:38:13 UTC | + properly shortcut out if there are no ERCC data - a user may supply an input that contains no ERCC data. Supplying a set of 0 alignment counts to the chi-squared / goodness-of-fit tests is a bad thing, and leads to odd warning cases. This logic will catch this scenario earlier, properly exit out, and give an informative message to the user. | 17 March 2015, 21:09:28 UTC |
| 87b99a2 | Indraniel Das | 17 March 2015, 16:34:19 UTC | + adjust the chi-squared test inputs - don't use run the tests on the log of the Alignment Counts, rather scale the alignment counts by a factor of 10000. This reduced number will allow for greater variability on the alignment counts. - remove the epsilon logic, we don't need it anymore now that the logarithms aren't being used anymore. This was introduced for fault tolerance, a log(0) is undefined. | 17 March 2015, 21:09:28 UTC |
| 997f6de | Indraniel Das | 17 March 2015, 04:34:27 UTC | + adjust the labels on the linearity plot | 17 March 2015, 21:09:27 UTC |
| 9216699 | Indraniel Das | 17 March 2015, 04:27:40 UTC | + clean up R script code - place option processing into its own function - place the main logic into its own function - remove comment code section at the bottom of the file - add comment section headers | 17 March 2015, 21:09:27 UTC |
| a3714e5 | Indraniel Das | 16 March 2015, 17:39:51 UTC | + some initial analysis refactoring work | 17 March 2015, 21:09:26 UTC |
| 4315958 | Eddie Belter | 17 March 2015, 20:42:06 UTC | InstData Import: make anp required in workflow step | 17 March 2015, 20:42:06 UTC |
| b9f60f5 | David Morton | 17 March 2015, 19:58:20 UTC | Merge pull request #565 from davidlmorton/ccsvcf-optional-process Make process optional (to allow cmd line to work) | 17 March 2015, 19:58:20 UTC |
| d9a5397 | dmorton | 17 March 2015, 19:48:33 UTC | Revert "Commit Process before launching workflow" Turns out that the only SR that this Process is the requestor for is created in this process, not in the workflow that this process launches. This reverts commit ebc75b0b735ea1c203e068d4085d45581014892b. | 17 March 2015, 19:48:33 UTC |
| 1503266 | Eddie Belter | 17 March 2015, 19:25:03 UTC | Merge pull request #498 from ebelter/sample-import-7 Remove Sample Importer | 17 March 2015, 19:25:03 UTC |
| 9bad6aa | Eddie Belter | 17 March 2015, 19:23:02 UTC | Merge pull request #560 from ebelter/library-importer InstData: Generator commands to create entities and source files tsv | 17 March 2015, 19:23:02 UTC |
| f116207 | Indraniel | 17 March 2015, 19:19:37 UTC | Merge pull request #557 from indraniel/ercc-map-unaligned-experiment-pt1 ERCC-based Quality Control Screening for RNASeq: Part 1 | 17 March 2015, 19:19:37 UTC |
| 65e4de1 | Thomas Mooney | 17 March 2015, 19:01:30 UTC | Whitespace. | 17 March 2015, 19:01:30 UTC |
| ebc75b0 | dmorton | 17 March 2015, 19:00:05 UTC | Commit Process before launching workflow | 17 March 2015, 19:00:05 UTC |
| 821c12d | Thomas Mooney | 17 March 2015, 18:58:01 UTC | Should now support >2 refiners if needed. | 17 March 2015, 18:58:01 UTC |
| 05fc93f | Thomas Mooney | 17 March 2015, 18:46:37 UTC | Move "operation" subs only used by Align. | 17 March 2015, 18:46:37 UTC |
| 4514e1d | Thomas Mooney | 17 March 2015, 18:38:49 UTC | Merge group determination now only in Generator. | 17 March 2015, 18:38:49 UTC |
| de8500a | Thomas Mooney | 17 March 2015, 18:36:53 UTC | Refiner key now only needed inside Refine. | 17 March 2015, 18:36:53 UTC |
| cf6eb88 | Thomas Mooney | 17 March 2015, 18:30:02 UTC | Keep ordered groups of refinements. | 17 March 2015, 18:30:02 UTC |
| d8d2fe9 | Thomas Mooney | 17 March 2015, 18:19:50 UTC | Remove breakpoint. | 17 March 2015, 18:19:50 UTC |
| 3ab344f | Thomas Mooney | 17 March 2015, 17:03:50 UTC | Only generate for one group at a time. | 17 March 2015, 17:03:50 UTC |
| e421f47 | Yevgeniy Gindin | 17 March 2015, 16:16:47 UTC | Merge pull request #510 from ygindin/master Created methylation_ratio | 17 March 2015, 16:16:47 UTC |
| 6e3427b | Thomas Mooney | 17 March 2015, 16:00:50 UTC | Perform the grouping in advance. | 17 March 2015, 16:00:50 UTC |
| 3262ca7 | David Morton | 17 March 2015, 14:55:54 UTC | Merge pull request #564 from dufeiyu/bug_fix Make Htseq count to revivify the per lane bam from merged bam | 17 March 2015, 14:55:54 UTC |
| 310a3bb | Indraniel Das | 16 March 2015, 23:38:44 UTC | + apply @nnutter 11th recommendataion (PR 557) - after a discussion with @nnutter, I'm going to try out the SKIP approach on the test associated with this tool. | 16 March 2015, 23:38:44 UTC |
| a4e2be6 | Indraniel Das | 16 March 2015, 23:37:05 UTC | + apply @nnutter 10th recommendataion (PR 557) - actually use the $self->pdf_file attribute in the code This parameter is supplied as an option parameter to the R script that's called internally. - additionally return the R analysis script as a Path::Class object. | 16 March 2015, 23:37:05 UTC |
| b3d2a71 | Indraniel Das | 16 March 2015, 23:34:26 UTC | + apply @nnutter 9th recommendataion (PR 557) - be more explicit on the option documentation for the ercc_spike_in_mix parameter. | 16 March 2015, 23:34:26 UTC |
| 642c344 | Indraniel Das | 16 March 2015, 23:32:39 UTC | + apply @nnutter 8th recommendataion (PR 557) - use the FilePath attribute on the errc_spike_in_file input param, and the pdf_file output param in the Genome class defintion. | 16 March 2015, 23:32:39 UTC |
| 006c6b6 | Indraniel Das | 16 March 2015, 23:30:48 UTC | + apply @nnutter 7th recommendataion (PR 557) - don't allow Path::Class to import functions into the namespace | 16 March 2015, 23:30:48 UTC |
| 3459f61 | Nathaniel Nutter | 16 March 2015, 23:20:21 UTC | Merge pull request #559 from nnutter/RT-104532 support importing "new" Nimblegen capture/primary split bed files | 16 March 2015, 23:20:21 UTC |
| 922d49b | dmorton | 16 March 2015, 20:26:00 UTC | Remove process from subclass description Since process is already declared in the parent class as 'transient' and 'optional' this declaration is redundant. | 16 March 2015, 20:26:00 UTC |
| e260743 | Jason Walker | 16 March 2015, 20:01:23 UTC | Merge pull request #558 from jasonwalker80/de_optional_cummerbund DE - cummeRbund optional | 16 March 2015, 20:01:23 UTC |
| 9312185 | dmorton | 16 March 2015, 19:42:03 UTC | Make process optional (to allow cmd line to work) | 16 March 2015, 19:42:03 UTC |
| 1f488c1 | Nathaniel Nutter | 16 March 2015, 19:08:29 UTC | remove use of capture/primary in names | 16 March 2015, 19:13:47 UTC |
| b3cbed6 | Nathaniel Nutter | 16 March 2015, 19:01:58 UTC | remove chromosome name "fixing" code | 16 March 2015, 19:01:58 UTC |
| 4736663 | Thomas Mooney | 16 March 2015, 19:01:53 UTC | Process one instrument data at a time. (Prepare for grouping.) | 16 March 2015, 19:01:53 UTC |
| a5ba4de | Nathaniel Nutter | 16 March 2015, 19:00:14 UTC | remove description since FeatureList ignores it anyway | 16 March 2015, 19:00:14 UTC |
| 220f459 | Thomas Mooney | 16 March 2015, 17:56:05 UTC | Split G:ID:Composite::Workflow into "generators" for the different parts | 16 March 2015, 17:56:05 UTC |
| 4ebc334 | Indraniel Das | 16 March 2015, 17:52:00 UTC | + apply @tmooney bowtie2 path usage suggestion See https://github.com/genome/genome/pull/557/files#r26489082 | 16 March 2015, 17:52:00 UTC |
